PoPoolation trimming pipeline
PoPoolationis a toolkit for handling Pool-Seq data, which includes a Perl script for performing a trimming pipeline similar to the one implemented here (trim-fastq.pl).
All features implemented in that script could be mimic in TrimReads to apply the same trimming pipeline.
Differences
The correspondence between arguments is the following:
| PoPoolation | TrimReads | Note |
|---|---|---|
| Default | Default | ReadTools does not output single end in a separate file yet. This may be solved in the future |
--no-trim-quality |
--disableTrimmer MottQualityTrimmer |
|
--min-length |
--minReadLength |
|
--no-5p-trim |
--disable5pTrim |
|
--quality-threshold |
--mottQualityThreshold |
|
--discard-internal-N |
--readFilter AmbiguousBaseReadFilter --ambigFilterFrac 0 |
This option is behaving slightly different. PoPoolation applies this filter before trimming the quality and TrimReads apply it afterwards |